end<start for empty sequences in Sequence[] from SeqCigar[]

[jalview.git] / src / vamsas / objects / simple / MsaResult.java

diff --git a/src/vamsas/objects/simple/MsaResult.java b/src/vamsas/objects/simple/MsaResult.java
index 97000e4..43a8c6e 100755 (executable)
--- a/src/vamsas/objects/simple/MsaResult.java
+++ b/src/vamsas/objects/simple/MsaResult.java
@@ -3,72 +3,104 @@
  *
  * This file was auto-generated from WSDL
  * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
-package vamsas.objects.simple;
-
-public class MsaResult  extends vamsas.objects.simple.Result  implements java.io.Serializable {
-    private vamsas.objects.simple.Alignment msa;
-
-    public MsaResult() {
-    }
-
-    public MsaResult(
-           vamsas.objects.simple.Alignment msa) {
-           this.msa = msa;
-    }
-
-
+ */\r
+\r
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+*/\r
+package vamsas.objects.simple;\r
+\r
+public class MsaResult extends vamsas.objects.simple.Result\r
+    implements java.io.Serializable {\r
+    private vamsas.objects.simple.Alignment msa;\r
+    private java.lang.Object __equalsCalc = null;\r
+    private boolean __hashCodeCalc = false;\r
+\r
+    public MsaResult() {\r
+    }\r
+\r
+    public MsaResult(vamsas.objects.simple.Alignment msa) {\r
+        this.msa = msa;\r
+    }\r
+\r
     /**
-     * Gets the msa value for this MsaResult.
-     * 
-     * @return msa
-     */
-    public vamsas.objects.simple.Alignment getMsa() {
-        return msa;
-    }
-
-
+ * Gets the msa value for this MsaResult.
+ *
+ * @return msa
+ */\r
+    public vamsas.objects.simple.Alignment getMsa() {\r
+        return msa;\r
+    }\r
+\r
     /**
-     * Sets the msa value for this MsaResult.
-     * 
-     * @param msa
-     */
-    public void setMsa(vamsas.objects.simple.Alignment msa) {
-        this.msa = msa;
-    }
-
-    private java.lang.Object __equalsCalc = null;
-    public synchronized boolean equals(java.lang.Object obj) {
-        if (!(obj instanceof MsaResult)) return false;
-        MsaResult other = (MsaResult) obj;
-        if (obj == null) return false;
-        if (this == obj) return true;
-        if (__equalsCalc != null) {
-            return (__equalsCalc == obj);
-        }
-        __equalsCalc = obj;
-        boolean _equals;
-        _equals = super.equals(obj) && 
-            ((this.msa==null && other.getMsa()==null) || 
-             (this.msa!=null &&
-              this.msa.equals(other.getMsa())));
-        __equalsCalc = null;
-        return _equals;
-    }
-
-    private boolean __hashCodeCalc = false;
-    public synchronized int hashCode() {
-        if (__hashCodeCalc) {
-            return 0;
-        }
-        __hashCodeCalc = true;
-        int _hashCode = super.hashCode();
-        if (getMsa() != null) {
-            _hashCode += getMsa().hashCode();
-        }
-        __hashCodeCalc = false;
-        return _hashCode;
-    }
-
-}
+ * Sets the msa value for this MsaResult.
+ *
+ * @param msa
+ */\r
+    public void setMsa(vamsas.objects.simple.Alignment msa) {\r
+        this.msa = msa;\r
+    }\r
+\r
+    public synchronized boolean equals(java.lang.Object obj) {\r
+        if (!(obj instanceof MsaResult)) {\r
+            return false;\r
+        }\r
+\r
+        MsaResult other = (MsaResult) obj;\r
+\r
+        if (obj == null) {\r
+            return false;\r
+        }\r
+\r
+        if (this == obj) {\r
+            return true;\r
+        }\r
+\r
+        if (__equalsCalc != null) {\r
+            return (__equalsCalc == obj);\r
+        }\r
+\r
+        __equalsCalc = obj;\r
+\r
+        boolean _equals;\r
+        _equals = super.equals(obj) &&\r
+            (((this.msa == null) && (other.getMsa() == null)) ||\r
+            ((this.msa != null) && this.msa.equals(other.getMsa())));\r
+        __equalsCalc = null;\r
+\r
+        return _equals;\r
+    }\r
+\r
+    public synchronized int hashCode() {\r
+        if (__hashCodeCalc) {\r
+            return 0;\r
+        }\r
+\r
+        __hashCodeCalc = true;\r
+\r
+        int _hashCode = super.hashCode();\r
+\r
+        if (getMsa() != null) {\r
+            _hashCode += getMsa().hashCode();\r
+        }\r
+\r
+        __hashCodeCalc = false;\r
+\r
+        return _hashCode;\r
+    }\r
+}\r